I hope that I’ve presented a compelling argument for evolution so far, which would by default also present a compelling argument against young-earth creationism. What I haven’t addressed yet is intelligent design, and for good reason. Intelligent design is a tricky think to pin down; it means different things to different people, from a “dba” for creationism to what is essentially evolution with a prime mover (which is, I believe, the Catholic stance). Since I’ve already addressed creationism, for the purpose of this essay I’ll treat intelligent design as “intelligent evolution” – that is, evolution with a deific catalyst and guiding hand. I’ll treat the god involved as a stand-in for the Christian God, who has the properties of being all-knowing, all-powerful, and good. The arguments against a demiurge like Gaia, Ptah, or Marduk are more difficult to address, since you need to be able to definitively list the attributes of a god to present counter-evidence.

I’ve also avoided intelligent design so far because I don’t think it’s diametrically opposed to evolution, and evolution was meant to be the scope of the essay. You can be convinced of evolution and still be a good Christian. You can be convinced of evolution and still be a good many things; since the theory of evolution doesn’t speak to abiogenesis or the origin of the universe or ethics, or even body-soul duality. But I think that that once a person has made a study of evolution and accepted the basic tenets, they can make arguments – convincing arguments – against a deistic demiurge. Consider this chapter, if you will, an appendix to the rest of the essay.

I think it’s important first to give attention to what I believe are the primary arguments for intelligent design (and if I’m presenting them unfairly or missing any substantial arguments, as always please let me know!): The fine-tuning of the universe, and the Watchmaker hypothesis.

The fine-tuned universe(http://en.wikipedia.org/wiki/Fine-tuned_Universe) theory suggests that the fundamental physical constants (the speed of light, the size of the electric charge of the electron, the relative mass of electron to proton, etc.) are tuned to a very narrow band, where altering them even by a couple of percentage points would preclude the possibility of life as we know it. Stars would not form, so heavier elements like oxygen and carbon (much less iron) would be incredibly scarce, and there would be no chance of finding protein, much less life.

There are a three significant responses:

First, that the universe isn’t as fine tuned as we’ve been led to believe, at least from a cosmological perspective (http://en.wikipedia.org/wiki/Fine-tuned_Universe#Disputes_on_the_extent_and_existence_of_fine-tuning) The “goldilocks” bands in these constants within which stars could form is quite a bit wider than has been claimed, and once you have stars performing fusion you get heavier elements, and the rest is abiogenesis and evolution. Of course, this response is based on mathematical models and not practical experience (nobody is running around varying universal constants in laboratories and trying to spark stars into existence), but so is the original claim.

Second, if the universe is fine-tuned, it could be the expected result of cosmologically-scaled evolution. Just as species tend to produce viable offspring (or they wouldn’t be species for long!) universes produces viable baby universes. This argument relies on the concept that black holes are spouting baby universes in new dimensions, which is questionable at best. Still, the fine-tuning mentioned is actually tuned to create stars; carbon-based life is only an interesting by-product. Stars beget black holes, and black holes beget universes with the same constants as the parent universe (excepting, perhaps, some cosmologically-scaled genetic mutation). Thus, our universe exists with the constants it has because universes with those constants are most likely to reproduce. Purely in terms of statistics, we’re most likely to find ourselves in a universe that can sustain stars, and thus life.

The third response says, “Of course we find ourselves in a universe that’s able to sustain life, if we didn’t, we wouldn’t be having this conversation, would we?” This is generally referred to as the Anthropic Principle (http://en.wikipedia.org/wiki/Anthropic_principle). This response recalls the statistical discussion in a previous chapter about the likelihood of your parents producing you – the chance you’d come out as you are is astronomically small, but you were going to be like somebody one way or the other, and the you that popped out won the lottery, so it’s too late to argue now. Douglas Adams had an amusing take on how this concept of fine-tuning works (as quoted by Richard Dawkins):

… imagine a puddle waking up one morning and thinking, ‘This is an interesting world I find myself in, an interesting hole I find myself in, fits me rather neatly, doesn’t it? In fact it fits me staggeringly well, must have been made to have me in it!’ This is such a powerful idea that as the sun rises in the sky and the air heats up and as, gradually, the puddle gets smaller and smaller, it’s still frantically hanging on to the notion that everything’s going to be all right, because this world was meant to have him in it, was built to have him in it; so the moment he disappears catches him rather by surprise. I think this may be something we need to be on the watch out for.

The watchmaker analogy is an argument for the existence of a creator god that is at least as old as 1686, but is quoted most commonly in the words of William Paley:

In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there; I might possibly answer, that, for anything I knew to the contrary, it had lain there forever: nor would it perhaps be very easy to show the absurdity of this answer. But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer I had before given, that for anything I knew, the watch might have always been there. (…) There must have existed, at some time, and at some place or other, an artificer or artificers, who formed [the watch] for the purpose which we find it actually to answer; who comprehended its construction, and designed its use. (…) Every indication of contrivance, every manifestation of design, which existed in the watch, exists in the works of nature; with the difference, on the side of nature, of being greater or more, and that in a degree which exceeds all computation.

But the watchmaker analogy is not really an argument; it’s a rhetorical device meant to establish the plausibility of the statement that you can tell, simply by looking at something, whether or not it was the product of intelligent design on the basis of its orderliness versus complexity. Ignoring the obvious problem of the teleology of a watch versus that of a human, the problem with this argument arises when it is applied as equally to vestigial structures and other evolutionary quirks as to items of so-called “irreducible complexity” (“so-called because of the previous chapter’s discussion). Consider, for example, the number of vestigial features in humans. Just a starter:

Goose bumps(http://en.wikipedia.org/wiki/Goose_bumps#Anatomy_and_biology) are an involuntary reflex to cold or strong emotion. In other mammals, goose bumps have the useful feature of making the creature appear larger, or of trapping an insulated layer of air against the skin. In humans, there is no benefit. In fact, the feature is uncommon on our head and genitals, where we actually have hair.

Jacobsen’s organ (or the vomeronasal organ; http://en.wikipedia.org/wiki/Jacobsen%27s_organ#In_human_beings) is the chemoreceptor in the nose of many mammals that allows them to detect pheremones. There is still some debate over whether the organ exists in adult humans (though much less over whether it exists in fetuses, then atrophies), but there is agreement that there are no nerve pathways to the brain in humans – that is, even if it remains unatrophied in adults, it can’t be used. The area of the gene that codes for it has become non-functioning in humans.

Darwin’s tubercule(http://en.wikipedia.org/wiki/Darwin’s_tubercle) is that little point on the back of your ear. In humans it has no function; in other mammals it provides necessary structural support for a pointed ear. Meanwhile, it’s worth noting that just as many mammals have muscles that allow them to move and rotate their ears, so do humans. In the case of (most) humans, however, those muscles are atrophied, connect to nothing, and are non-functional.

The plantaris muscle (http://en.wikipedia.org/wiki/Plantaris_muscle) that runs under our foot is a very useful muscle for primates that grasp with all four limbs. In humans the muscle is so atrophied it is frequently mistaken for a nerve by medical students, and so useless that it is generally the first thing to be harvested for tendon reconstruction elsewhere in the body. The palmaris muscle is a similar structure in our hands.

The third eyelid (or nictitating membrane; http://en.wikipedia.org/wiki/Third_eyelid) is the transparent third eyelid common birds and reptiles that provides their eye protection from flailing prey and moisture during long staring sessions, but without cutting off vision. It’s found in some mammals as well (camels, polar bears, and seals, for example); dogs and cats have them, but theirs are not well-muscled, so you usually only see them when the animal is waking up from sleep. Humans also have a vestigial remnant of this third eyelid, but it’s functionless.

The male nipple. I’ll just leave that there.

Our five toes – or, specifically, our fifth toe appears to be a vestigial feature. It’s an extra thing to be broken or at least stubbed (as I reminded myself this morning), yet removing the pinkie toe doesn’t cause any loss of functionality or balance, and quite a few people put almost no weight on that toe when they walk. It’s a liability. Most other walking creatures have only four toes on the ground (consider the near-ubiquitous dewclaw in quadruped mammals – another example of vestigiality), but primates who grasp with their foot find their fifth toe as useful as we do our pinkie finger. And since our ancestors were primates, we get a fifth toe.

Likewise, the coccyx (or tailbone) is vestigial in humans, and a small number of people are borne with atavistic tails in its place. While the coccyx still has nine muscles attached to it, including one necessary for defecation, these can be successfully reattached to the sacrum with no loss of functionality (something, presumably, an intelligent designer could have done easily). What do we get for having a coccyx? Only the very painful possibility of a fracture.

Going back to our watchmaker analogy, what would you say, upon opening a watch, if you found mounting points for a different type of mechanism, gears with unused ratios, or a gap where previous models had used a winding spring instead of a battery? Probably nothing, because we’re used to this kind of re-use – it’s cheaper, it’s easier and it allows the manufacturer to save on the costs of retooling parts and redesign. But what kind of god does this? An all-powerful god, for whom a new design is no more difficult or costly than re-use? A god who sees the future and the end of all things, but fills our anatomy and genome with countless dead ends? Is it fair to call this god “lazy”? Was this god busy with something else, or disinterested? Are this god’s eyes truly on every sparrow? Aside from a brief mention of ERV’s in a previous chapter, we have not even addressed the cases where inclusion of these vestigial features poses us a real danger.

Think of our wisdom teeth, which helped our pre-agricultural ancestors chew cellulose – plant fibers in grass and leaves. When you have a diet like that, the more teeth the better! But our modern jaws aren’t as large as those of our ancestor species, so we run into the problem of impacted wisdom teeth. Estimates on the number of Americans with at least one impacted wisdom tooth run as high as 90%; extraction of wisdom teeth is now a routine procedure. Pain is generally the worst problem a person with an impaction is likely to face these days (with our better dental hygiene), but in the past the combination of partial eruptions and caries could lead to advanced tooth rot (and potentially fatal complications), and that does not count the (smaller) possibility of developing a malignant tumor at the site of the impaction (about 1-2% of all impactions, per wikipedia: http://en.wikipedia.org/wiki/Wisdom_tooth).

Think of your appendix, which also seems to have been useful in the past for digesting cellulose. (There are some claims that the appendix plays a role in our immune system, but this is not born out in decreased immune function among those who have had an appendectomy.) Acute appendicitis has a high mortality rate, and it affects about 7% of Americans over the course of their lifetime.

Were these oversights on a creator god’s part, or was that god worrying more of our plant-eating ancestors than modern humans? These might sound like sarcastic questions, but they are serious. What would you think of a human designer proposing these same features? So, If the watchmaker analogy holds, what do these kinds of designs say about the designer?

Consider the route of the vas deferens (http://upload.wikimedia.org/wikipedia/commons/0/08/Route_of_vas_deferens_from_testis_to_the_penis.png), which rises up from the testes to loop over the ureters, then descend past the bladder to the penis. In our ancestor species, the testes were internal (that’s the case for most mammals and other animals in general); as they descended to their modern external location, the vas deferens was “hooked” on the ureter, like a leash is hooked on a tree when a dog and its owner choose to walk on different sides. Would not a creator god have prevented this complication, and prevented subsequent cases of infertility and ureter obstruction (and subsequent infection?)

Consider, too, the route of the recurrent laryngeal nerve (http://en.wikipedia.org/wiki/File:Gray622.png), which allows us to speak (and allows other animals to vocalize). It leaves the brain, travels all the way down the neck, loops under the aorta, then travels back up to the larynx, taking more than a foot to accomplish what the superior laryngeal nerve does in inches. (Note especially the image here: http://www.icr.org/article/recurrent-laryngeal-nerve-not-evidence/). This is common in all mammals, so as you might imagine, in giraffes this creates a nerve pathway nearly fourteen feet longer than it needs to be! The second link above, as well as http://creation.com/recurrent-laryngeal-nerve and http://www.evolutionnews.org/2010/10/the_recurrent_laryngeal_nerve_039201.html argue that this is not bad design, because this nerve also enervates the heart and trachea along the way (though they do not address why it wouldn’t be a better design for the vagus nerve to enervate those, since it’s going down there anyway, or for the laryngeal nerve to continue on that way after passing the larynx, rather than looping back to make the larynx the final destination), or because redundant pathways provide backups (though they do not address why a simple left-right redundancy would not suffice, or that a looped pathway provides multiple points of failure to a critical organ), or because human circuit design is frequently circuitous (though they do not seem to realize this exposes their god to claims of limited resources or lazy design). From a strictly evolutionary viewpoint, the route makes sense. Our distant ancestors, fish, have no larynx or even a neck, but they use the same nerve to enervate their gills. As the laryngeal function developed in the trachea, it is understandable that nerves which serve the respiratory system would continue to serve new features there; the unfortunate consequence in mammals is the location of the voicebox at the top of the throat and a nerve that couldn’t come untangled from the aorta. Would not a perfectly intelligent designer have foreseen this consequence and disentangled them to begin with?

One could argue that the ways of a designer are mysterious and beyond our comprehension, but what does that tell us? If we were made in the image of the designer even on a metaphorical level, should not the watchmaker analogy hold, and we would recognize both excellent and poor design? Wouldn’t we expect to see upright human posture supported by a spine and bones ready-made for such a position, rather than an unstable adaptation from a quadrupedal posture? (http://www.fireandknowledge.org/archives/2007/12/22/our-imperfect-backbone-miller/) Or does the watchmaker analogy fail, and we cannot differentiate intentional design from evolutionary “mistakes”?

Evolution’s design is an emergent quality of semi-random events, so it makes sense both that we’d see re-use of homologous features like the pentadactyl limb and complete redevelopment of the same feature (like eyes, which have evolved independently at least fifty different times (http://en.wikipedia.org/wiki/Evolution_of_the_eye, and sometimes better than others). Why would a creator god choose to cobble a panda “thumb” (pronounced as “wrist-spike”) from of a sesamoid bone (http://en.wikipedia.org/wiki/Sesamoid_bone#Panda_anatomy) rather than just giving the panda the articulating opposable digit already available in other creatures that need to grasp?

Any of these arguments, taken individually, could be marginalized, but I hope I’ve presented a sufficient number of them to establish a pattern – a pattern whose reasonable conclusion requires increasingly complex logical gymnastics to avoid. These may not constitute an argument against gods in general, but in general it’s impossible to conclusively prove the non-existence of a thing. (That holds for both gods and celestial teapots (http://en.wikipedia.org/wiki/Russell%27s_teapot).) What I hope I’ve done is show that if a creator god is assumed to have the certain characteristics of the Christian God, the evidence that suggests naturalistic evolution overwhelms the evidence that suggests intelligent design by such a god.

In closing, think for a little bit about the size of the universe – really think about it. As many times as I do it, it’s still mind-boggling. http://www.youtube.com/watch?v=17jymDn0W6U. About the biggest number I can deal with in my head is the number of people in a packed stadium – say about 40,000 people. That’s about the population of a moderately-sized city, or more than 250 times the number of people a person can reasonably be expected to interact with and know (http://en.wikipedia.org/wiki/Dunbar’s_number). You need a block of these packed stadiums, five long and five deep, to hold a million people. (Already my mind’s grasp on the scale is beginning to slip.) You need 7,000 such blocks blocks (think 70 wide, 100 deep) to hold the number of people living in the world today. That’s just people. We may be pretty smart, and we may have a massive impact on our planet, but there are probably about 100,000 ants alive for every human alive. And that’s not even counting whales and horses and three-spined sticklebacks and all of the other multi-cellular creatures. There’s lots of those. So that’s a huge number, but just a drop in the bucket compared to the number of bacteria, which is probably around five million trillion trillion (or five with thirty zeroes after it). That’s a huge number, but that’s just Earth, which is just one rock orbiting a pretty unremarkable star. Back of the napkin math suggests that there are one hundred stars in the universe for every grain of sand on every beach on Earth.

How can we even begin to take seriously any theory that suggests we’re the center of things?

In this chapter of the essay, I’m going to try to address common arguments against evolution. A few of these arguments I chose based on previous conversations but in order to make sure that I was fairly seeking out the best, most reasonable arguments against evolution, I posted threads on several forums and on facebook requesting those who don’t believe in evolution to link to or explain their best arguments. Unfortunately I had no takers. (This probably says more for my poor choice in forums than a lack of available arguments.) To fill the gaps, I’ve distilled the arguments from the top search results for “arguments against evolution” (avoiding pro-evolution sites that are addressing the arguments). My attempt in distilling these arguments has been to use a selective filter only so far as to include actual arguments against evolution instead of appeals to scripture. That said, if I’ve missed any arguments against evolution that seem persuasive to you, please let me know so I can attempt to address them here or admit that I cannot. If you do propose an argument, though, please be familiar with it yourself – don’t just link me to an endless page of opposition. Tell me what you think doesn’t make sense.

Scientists can’t agree on or prove how the universe formed.
This is essentially true (though it would be incredibly untrue to say that there isn’t a general consensus regarding the big bang and the expansion of the universe, and it would deceptive not to say that recent study has born out the general theory, though specifics are still being debated). That said, the argument doesn’t say anything about evolution. It is a general logical error to say that because the theory of creation contains an origin story for the universe, that evolution must also. Consider, again, that the Catholic Church embraces both a creator god and evolution. If, however, you’d like to argue the relative merits of creationism versus the big bang theory, we can address that in a different thread. If you’d like to read more about the big bang, the following are good places to start: http://en.wikipedia.org/wiki/Big_bang, http://www.talkorigins.org/faqs/astronomy/bigbang.html

Scientists can’t agree on/prove how chemicals became life.
While we’re closer to evolution here because we’re now dealing with life, the theories surrounding abiogenesis also do not speak to evolution. Again, while creationism addresses the origin of life, evolution does not. The two theories do not map equally. If you’d like to read more about abiogenesis, the following are good places to start: http://en.wikipedia.org/wiki/Abiogenesis, http://www.talkorigins.org/faqs/abioprob/

Evolution is statistically impossible.
A common anti-evolution argument is that cellular life is statistically improbable: the chance of all of the proteins necessary even a simple bacterium self-assembling in a single place is so minute as to require an Earth 100 billion years old before we’re even within the realms of possibility; not only that, but if it were statistically possible, why don’t we see life reappearing across earth? As it’s stated, this objection is actually just a subset of the previous argument about abiogenesis, but the concept is worth dealing with anyway.

Firstly, something does not have to be statistically probable to be true. If your parents’ gametes could have produced up to 100 million different possible combinations (as we discussed in the first chapter), the chance that you are the one that would result is infinitesimally small – your parents would have had to have had a child every year for 10 million years to even have a 10% chance of producing you. If there are 10 quadrillion possible viable human genetic combinations (as previously discussed), and about 100 billion humans have lived, the chance of you being produced by any set of parents is roughly 1 in 100,000 – very poor odds indeed. And yet here you are!

Secondly (and now that I’m done being flippant with statistics), the argument doesn’t take a number of important details into consideration. Firstly, the case study for the argument – a minimal but modern bacteria called Mycobacterium genetalium which has about 400 different proteins – only needs about 256 of those proteins to survive. Even that very simple bacterium, though, is on an order of complexity several magnitudes beyond what abiogenetists propose as the first protocells (consider, for example, the difference between viruses and bacteria). The argument ignores the fact that these 400 proteins are created from peptide building blocks that do self-assemble easily and quickly in laboratory tests do to the chemical properties of the molecules involved, and that only the simplest need have assembled to produce protolife – the more complex proteins build off the others as the protolife becomes more complex. In other words, the process is not random, any more than coins appearing in the correct slots in a coin sorter is random – conditions can favor certain results (likewise, in my flippant example above, the chance of you being produced by your parents is far greater than the “completely random 1 in 100 million”).

The question about why we don’t see abiogenesis happening frequently today is more subtle. In response: firstly, conditions were different. There was little to no molecular oxygen available on the early Earth; oxygen is highly reactive and breaks down unbound complex molecules (in fact, oxygen would have been a potent poison to early life). Because there wasn’t life on the early earth, there weren’t bacteria just waiting to pounce on complex molecules as they would today – protolife would almost certainly be a favorite foodstuff of cellular creatures that encountered it. Secondly, it’s not particularly surprising that even under idealized laboratory conditions abiogenesis has not reoccurred – not compared with the billions of years and entire planet worth of chemicals available the first time it happened. That said, there have been some very promising test results, not just in producing amino acids spontaneously in early earth conditions (the famous Miller-Urey experiment: http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment), but in spontaneous production of RNA: (http://www.wired.com/wiredscience/2009/05/ribonucleotides/, http://en.wikipedia.org/wiki/RNA_world_hypothesis#Support_and_difficulties).

We might argue, too, that even with the building blocks of RNA spontaneously appearing, the chance of useful data appearing in their assembly is as slim as the likelihood that the proverbial room full of monkeys will type out Shakespeare. However, note (just for example) that of all the possible random combinations of 220 nucleotides, “a staggering 2.5 x 10112 sequences are efficent ligases”. In other words, the chances are much more similar to a room full of monkeys tapping out recognizable words here and there, and that hardly seems like such an impossibility

The law of entropy precludes evolution
This argument is fairly easy to address. Most of those who employ this argument cite the 2nd law of thermodynamics, which in its oldest, most fundamental form states:
“No process is possible whose sole result is the transfer of heat from a body of lower temperature to a body of higher temperature.”

Of course, what is usually meant is the downstream corollary,
“The entropy of a closed system (such as the universe) tends toward a maximum”.

Problematically for this argument, the Earth is not a closed system. It is constantly being fed by energy, primarily from the sun, but also from the stars and the constant barrage of meteors and comets and dust. Feeding energy into a system can produce a variety of results, but one only needs to bake a cake to know that simply “getting hotter” is not the only result. Chemical changes occur in the presence of heat. Note, too, that the creation of heavier elements (an increase of energy level and order) depends on the disordered fusion of hydrogen, and that this is going on constantly inside our sun. Note further the chemists’ corollary to the 2nd law:
“Energetically, the second law of thermodynamics favors the formation of the majority of all known complex and ordered chemical compounds directly from their simpler elements. Thus, contrary to popular opinion, the second law does not dictate the decrease of ordered structure by its predictions. It only demands a “spreading out” of energy when such ordered compounds are formed spontaneously.”

Some may argue that complex chemicals like chlorophyll require life or a “patterning mechanism” to appear, but just like RNA this is untrue – chlorophyll and many other complex chemicals do develop spontaneously in the lab. Organic processes are just much more efficient, exactly as we would expect.

Creatures do not gain new genetic information – they do not become more complex, they simply adapt or speciate within their “kind”
In essence, this is an argument that micro-evolution is granted, but macro-evolution is not. We may see black-caps diverge into two species of bird, or we may see proto-horse become horse, but we don’t see grasshoppers become elephants. Ignoring for the moment that there is significant evolution between the proto-horse and the horse (and even more so between proto-whale and whale!), and ignoring the fossil record in general, while we have observed “micro-evolution” and speciation (technically, speciation is macro-evolution) we would never expect direct observation of the kind of changes mentioned. If we saw a frog become a fish over even the course of 200 years, that would be evidence against evolution; it would falsify the predictions evolution makes. The only way we would expect to see that kind of transitioning between orders and classes is over millions of generatoins (i.e. – in the fossil record) and if the examples provided in previous chapters do not suffice, here is a feast of evidence: http://www.talkorigins.org/faqs/faq-transitional.html

Like begets like, and the vast majority of mutations are not favorable (two-headed calves, mermaid babies, Down syndrome, etc.)
There are several issues complicated together here. Firstly, the kinds of mutations mentioned above are not the type we’d expect to produce favorable results: firstly, they’re generally major chromosomal problems (like an extra or missing chromosome), not just the addition or modification of a genome. Secondly, those kinds of significant morphological changes (two heads or conjoined limbs) are too severe to re-enter the breeding pool – both people and animals both who suffer from significantly different appearances or constructions are much less likely to find mating partners. Much smaller changes (like the ability to process milk, a change in eye or hair or skin color, increased hardiness to cold or heat) are the kinds of mutations we do see happening at the genomic level, and these are likely to persist in the gene pool.

Secondly, the mechanism that allows for speciation requires that breeding pools are separated. Even if two-headed calves continued to breed normally with other cows, we wouldn’t expect them to speciate unless a particular herd in which two-headed calves appeared was separated from the rest over a very long period and two-headedness offered some advantage. Among humans there is no separate breeding pool that has existed for any notable period of time (more than 10,000 years or so), so the biggest changes we’re likely to see are minor morphologies like facial structure, eye and hair and skin color, shapes of fingernails, etc.

Thirdly, most mutations are neutral – they aren’t even noticed. Of the small portion that are noticeable and harmful, they are likely to be removed from the breeding population very quickly (as discussed above). However, those that are favorable are much more likely to persist. Therefore even if there are a hundred unfavorable mutations to every favorable mutation, the favorable mutations have a much more significant result over even a handful of generations, since they have the potential to propagate geometrically.

Creatures occurred fully developed in the Cambrian explosion without links to single-celled ancestors. There is no satisfying link between ape and man. Etc.
These issues have already been addressed in specific, but this is an opportunity to turn the argument around in general. How many examples of evolution have to be provided? Lack of evidence is grounds for lack of belief, but not alone grounds for belief in an alternate theory. If you accept the evidence for evolution between reptile and bird, between proto-horse and horse, between wasp and bee, but don’t find the evidence for evolution between single-celled organisms and crustaceans convincing, or don’t find the phylogenetics between apes and humans convincing, tell me which is more likely – that evolution occurs in some cases but not in others, or that the particular detail in the overall theory is not adequately evidenced? I would argue that the evidence in the mentioned cases is extremely compelling, but the point is that the theory of evolution is evidenced with thousands of examples, so does debate surrounding one or two of them (if it cannot be generalized to all of them, that is) shift the preponderance of the evidence?

Some complexity is irreducible. An eye is useless without its component parts. A bombardier beetle would self-immolate without all features in place.
Irreducible complexity is a fact – there are systems that will lose their function if any one part is removed, but it is not true that examples of these preclude evolution. Consider possible ways the system could have evolved: deletion of parts, addition of multiple parts, change of function, addition of a second function to a part, or gradual modification of all parts. Additionally, some systems once considered irreducibly complex might not be. Bacterial flagella were thought to be irreducibly complex, but we are now aware of bacteria with simpler versions of flagella (they are missing “required” component parts) or which use some of the structures in an entirely different, and apparently more primative way – for secretion.

To address the two cases specifically, Darwin’s quote that the evolution of the eye seems “absurd in the highest degree” is generally indicated as proof that it could not have evolved. What those who quote him fail to mention, though, is that he spent the next three pages explaining exactly the steps that could have produced the evolution of the eye:

photosensitive cell

aggregates of pigment cells without a nerve

an optic nerve surrounded by pigment cells and covered by translucent skin

pigment cells forming a small depression

pigment cells forming a deeper depression

the skin over the depression taking a lens shape

muscles allowing the lens to adjust

We know all of these steps are possible because they all exist in animals living today. We can even break these steps down further into smaller, intermediate steps and still find examples.

This is an argument from incredulity. It is based in part on an inaccurate description of how the beetle’s bombardier mechanism works, but even then the argument rests solely on the lack of even looking for evidence. In fact, an evolutionary pathway that accounts for the bombardier beetle is not hard to come up with (Isaak 1997). One plausible sequence (much abbreviated) is thus:

Insects produce quinones for tanning their cuticle. Quinones make them distasteful, so the insects evolve to produce more of them and to produce other defensive chemicals, including hydroquinones.

The insects evolve depressions for storing quinones and muscles for ejecting them onto their surface when threatened with being eaten. The depression becomes a reservoir with secretory glands supplying hydroquinones into it. This configuration exists in many beetles, including close relatives of bombardier beetles (Forsyth 1970).

Hydrogen peroxide becomes mixed with the hydroquinones. Catalases and peroxidases appear along the output passage of the reservoir, ensuring that more quinones appear in the exuded product.

More catalases and peroxidases are produced, generating oxygen and producing a foamy discharge, as in the bombardier beetle Metrius contractus (Eisner et al. 2000).

As the output passage becomes a hardened reaction chamber, still more catalases and peroxidases are produced, gradually becoming today’s bombardier beetles.

All of the steps are small or can be easily broken down into smaller ones, and all are probably selectively advantageous. Several of the intermediate stages are known to be viable by the fact that they exist in other living species.

If we evolved from monkeys, why are there still monkeys?
This argument is, on the face of it, silly enough to dismiss. Monkeys exist for the same reasons that your cousins exist – the fact that you were born does not preclude the existence of your parents or any of your relatives. Monkeys did not “turn into” humans any more than your parents turned into you.

However, there is a more subtle reading: wouldn’t evolution predict that the environmental forces that favored humans over their ancestors would have eliminated those ancestors? In fact, they did. No one proposes that humans came directly from chimpanzees, bonobos, rhesus monkeys, or any living species of primate – we are their distant cousins, more distant to some than others. We have a common ancestral species somewhere along the way, and that species is in fact extinct. When you read this question as “If we evolved from proto-humans, why are there still proto-humans”, we see that the obvious answer is that there aren’t. The species from which we evolved (discussed in a previous chapter) is extinct, and in at least the case of Neanderthal (a cousin,not an ancestor), we likely got rid of them either through too much war or too much loving – killing them off or interbreeding and absorbing them into our species. (Recall that closely related species, like wolf and coyote or lion and tiger can regularly produce viable hybrids.)

Evolution is not happening now. We don’t see transitional forms or new species appearing.
Evolution clearly is happening now, and we do see new species appearing – examples were given in previous chapters. To deny this you must redefine what “species” means. All we see are transitional forms – every species is either transitional or heading to a dead end. The reason we don’t notice this is because we don’t know what to expect of species in a few million years – if we did, we’d certainly note that our contemporary species were “transitional”, just like we do when comparing species that lived several million years ago to those that are modern.

Various quotes by famous scientists.
To treat them fairly, each quote has to be handled individually. Some are taken out of context (like Darwin’s remark about the eye), and some represent a poor understanding on the part of the scientist (like Hoyle’s remark about the probability of evolution). In all cases, though, an individual’s opinion is just that. It’s not evidence. When that individual publishes a paper with evidence backing up their opinion, it become evidence for or against the theory. Even if Darwin had recanted on his deathbed (he didn’t – http://www.talkorigins.org/indexcc/CG/CG001.html), it would not affect in any way the body of evidence gathered in the hundred and fifty years since.

While my interest in your arguments still stands, if you have a real interest in more substantial critique of most creationist/anti-evolutionary objections, this site is encyclopediac: http://www.talkorigins.org/indexcc/list.html

The fossil record, as mentioned above, is one of the most compelling bodies of evidence for evolution – that there are fossils of extinct species at all is interesting, that we can see where modern most genera first appear in the fossil records in the last few million years is amazing. We’ve recovered billions of fossils, from single cells to complete mammoths, from impressions left by ferns to the impressions of feathers surrounding an intact dinosaur skeleton.

And yet, the fossil record remains frustratingly sparse. We may have billions of fossils from hundreds of thousands of species, but there are likely as many as 25 million species of insects alive today. When you include other invertebrate and vertebrate animals, the number can only grow; when you include plants and single-celled organisms, the number skyrockets. Does this undermine the fossil record?

In a word, no. We expect the fossil record to be sparse relative to both the number of creatures and number of species that have ever existed. Fossilization is an extremely rare event – not only must the creature remain undisturbed after its death (already this is a severely limiting factor, if we expect ancient carnivores and carrion eaters to be as effective as their modern cousins), but they must also be almost immediately removed from the oxygen and bacteria that cause decomposition. (For example, they might be covered in a sandy landslide, or sink to the bottom of a peat bog). Once the creature has been removed from the immediate threat of decomposition, they still must encounter the unlikely conditions which allow the the skeleton (or other features) to mineralize; then, they must still remain undisturbed through thousands or millions of years of geological activity. Finally, and perhaps most unlikely, we have to be lucky enough to stumble across them. Aside from really exceptional fossil beds (http://en.wikipedia.org/wiki/Lagerst%C3%A4tte), fossils are generally rare, very difficult to access (thanks, solid rock!), and extremely expensive to extract and clean, without any of the lucrative payoff you get from other digging activities like diamond mining. We should perhaps be amazed that we have anything approaching a fossil record at all.

If we had only a single complete fossilized skeleton of an extinct creature, it wouldn’t do much to prove evolution. (A serious argument could be made for its effect on a creationist theory, however, and what an extinct species would have to say about the foreknowledge and power of a creator god, but disproving creationism is not the same as proving evolution.) Similarly, even thousands or millions of fossils of extinct species wouldn’t lend themselves to support for evolution if they did not first lend themselves to patterns – to patterns showing that a) the fossils actually represented stable species and not one-off mutations, and b) the species, genera, and families they represent show progression over time, as we’d expect in the “family tree” predicted by phylogenetics.

As to the first point, while there are certainly controversially taxonomied fossils (especially in the hominid line) clearly there are ample examples beyond controversy. We have more than thirty examples of Tyrannosaurus Rex (some skeletons complete or nearly so), more than 1200 specimens of just one species of smilodon, and Meganeura specimens (giant dragonflies) have been found in the UK, France, and the US, just to name a few examples. The second point, though – that we can see examples of “progression” (not in the sense of intentionally building toward a specific form, but in terms of a transition across forms from one morphology to something substantially different) – requires a bit more evidence.

Our modern horse, genus Equus, is a particularly interesting creature – even if for no other reason than its single-toed limbs. While the horse seems to have the same-shaped limb as most other mammals, it’s missing the eponymous feature of the “pentadactyl” limb – the five toes. We might suspect, though, that somewhere in its history, there is a horse ancestor – a proto-horse – with five toes. Interestingly, we have fossils of just such a species, along with many others that show a gradual transition from five toes to our modern single toe – as well as a gradual transition to grazing teeth and the skull structure of the modern horse. (You may wish to read through http://en.wikipedia.org/wiki/Evolution_of_the_horse for a more thorough discussion than I can manage here.)

We start about 52 million years ago (hereafter “mya”) with a creature called Hyracotherium (http://en.wikipedia.org/wiki/Hyracotherium), which looked something like a cross between a rabbit and a deer, about the size of a dog. (Note that Hyracotherium is definitely NOT a rabbit, as some have claimed: http://members.cox.net/ardipithecus/evol/lies/lie015.html. The original confusion that caused the species to be named “hyrax-like” occurred because the the initial naming occurred when only a few teeth – not even an entire skull – had been found) Hyracotherium had the five toes we’d expect in a mammal – four padded fingers and a fifth “thumb” off the ground, like a dog’s dewpad. Fast forward a few million years through the fossil record by means of Orohippus (50mya http://en.wikipedia.org/wiki/Orohippus), Epihippus (47mya http://en.wikipedia.org/wiki/Epihippus), Mesohippus (40mya http://en.wikipedia.org/wiki/Mesohippus), and Miohippus (36mya http://en.wikipedia.org/wiki/Miohippus), and we can watch several changes occurring gradually: the creatures grow larger, their teeth begin to adapt to grinding and chewing (i.e. they become grazing teeth), and our proto-horses begin to walk on only three toes – meanwhile, the first and fifth toes have become vestigial nubs.

Note three important points – first, each of the examples listed above are not single species but entire genera. There was no orderly escalator from Hyracotherium to modern Equus, but a series of branches constantly sub-branching. Our Equus is simply the highest point in a brambles of Equids. Secondly, each genus did not “replace” the one before it. Orohippus may have appeared only a couple of million years after Hyracotherium, but species of Hyracotherium thrived for up to 20 million years – in other words some species of Hyracotherium existed even after Miohippus had appeared. Lastly, the sample fossils that are used to define the genera are not proposed to be the specific ancestors of our modern horse – they are almost infinitely more likely to have been offshoot branches near the ancestors of the modern horse on the phylogenetic family tree. They show a general trend in progression, but they may also possess features that don’t continue through to future genera, like a changing number of vertebrae.

If you haven’t already, I highly recommend following the link to the wikipedia page on horse evolution (http://en.wikipedia.org/wiki/Evolution_of_the_horse), at least to see the pictures illustrating the gradual changes in toes and teeth from Hyracotherium through Equus.

The horse lineage is important evidence for evolution because while the difference between Hyracotherium and Equus is dramatic, an uncommonly populated fossil record shows gradual changes across many genera and millions of years accumulating to that dramatic difference. This evidence is particularly consistent with the theory of evolution, but does not fit well into a creationist theory that does not include evolution. And, while the horse lineage is probably the best documented, it’s certainly not the lineage in the fossil record.

Evolution of the Whale

The whale (and cetaceans in general) are a peculiar bunch – mammals who live entirely within the water, though they have to breathe air to live. If we didn’t already know they existed, we’d think they were unlikely even as science fiction, yet until the intervention of human over-hunting, cetaceans thrived. It’s clear that whales had terrestrial ancestors from the appearance of internalized, vestigialized features (like the “fingers” in their fins, the frequent floating bones of their now-missing hind legs, and the internal ear that now picks up sound from their jawbone), and while their lineage is not as well-documented as Equus, it is possible to trace back through proto-cetaceans to likely precursors of the whale (judged by unique features like ear construction and the shape of their teeth).

Again, the intent is not to show that these fossils were directly in the line of descent between a dog-like creature and our today’s Cetaceans, but rather that the creatures they represent show the transitional forms we’d expect between an Indohyus and a modern whale – that transitional forms exist and thrived during the times we’d expect. Whether a specific creature is or is not directly in the ancestral line is a detail for paleontologists to argue about, but doesn’t bear directly on the fact that transitional forms do exist.

There remains some considerable contention as to what branch of dinosaurs produced birds, or even if another upstream branch of reptiles called archosaurs were their ancestors, but there is no remaining doubt amongh those who study evolution that birds came from reptiles (or, as some would say, that they are still reptiles).

Humans

The evolution of humans is – at least between evolutionary theorists and creation theorists – the most contentious case study. However, because we’re a topic of great interest to ourselves, we’ve received a great deal of study from ourselves; more that can be usefully summarized here in a way that’s more convincing than the examples above. The fossil list (http://en.wikipedia.org/wiki/List_of_human_evolution_fossils) and the writeup of human evolution on Wikipedia (http://en.wikipedia.org/wiki/Human_evolution) are extensive, and worth at least a cursory glance if not careful study. The matter is complicated by the concept of human exceptionalism (http://en.wikipedia.org/wiki/Human_exceptionalism) – the idea that humans aren’t just part of the fauna – but once the human fossil records and history are compared to those of other species, it becomes more difficult to deny that humans have a history significantly different from other animals, and that exceptionalism is a matter of philosophy and psychology, and not genetics or biology.

Arguments against the Fossil Records as Evidence for Evolution

Several specific arguments were raised in comments on these posts, and I’ll address them directly here. (I note that there are in fact -countless- arguments against the fossil record in general and fossils in specific – many of them completely groundless, and many of them very relevant and worthy of engagement. Answering every argument is far outside the scope of this essay, but if there are any particular arguments you feel are persuasive and applicable, please direct me toward them.)

I can’t argue against the the fact that there are substantial gaps between the species we see in the fossil record when we fit them into the tree predicted by phylogenetics. The hypothetical “bough” in the link above shows a 3% fill rate, but I’d be surprised to see it even as high as 1%. But gaps in the fossil record are not evidence against evolution, nor do they undermine the theory in any way. Due to how uncommon fossilization is, we will always have gaps in the fossil record – even if we were able to excavate the entire Earth.

Still, if we have even one transitional form between two species – if we can draw even a very dotted line between two genera – we have evidence for evolution. But we have countless dotted lines, and some of them (like the horse), are less dotted and more solid.

The question is, how much accumulated evidence do you require before it becomes overwhelming? Once set, you cannot move your goalposts without sacrificing your dignity. A singled dotted line might be interesting but an outlier – a work of fancy rather than reason – but two or three are a pattern, and two or three hundred are substantial by any measure. The more fossils appear, the more gaps we will have between them since transitions are never as abrupt as a single generation. And the more fossils we find to fill the gaps, the more we may realign our theory about the descent about a particular line; but continued refining of the details of the theory does not affect the validity of the theory as a whole. We may not have even a dotted line for some genera, but if evolution is indicated for some, would a lack of intermediate fossils suggest two different forces in play – evolution for some, and divine creation for others?

The first argument does not take much to refute – there is evidence for both smooth transition and punctuated equilibrium (and, in fact, evidence that each occur in in difference scenarios; smooth transition as creatures refine competition to maximize a particular niche and punctuated equilibrium as creatures encounter new niches that have not been filled, as in the case of adaptive radiation), just as there is evidence on both sides of a number of current academic debates among those who study evolution. None of those debates undermine our understanding of evolution as a general theory, both sides of the debate are only refining aspects of evolution and require the basic tenets of evolution to make sense.

To say that ongoing academic debate about aspects of the theory becomes an argument against the theory in general is along the lines of encountering a debate between artists arguing if a particular shade is blue-green or aquamarine, and therefore proposing that colors do not exist and the shade is gray. The argument mentioned in particular is not “Evolution can only exist if in the form of punctuated equilibrium” or “Evolution can only exist if in the form of smooth transition” but “We have evidence for a greater frequency of smooth transition” and “We have evidence for a greater frequency of punctuated equilibrium” and then a debate following as to whose evidence could in fact be reinterpreted in the light of the other’s understanding.

As mentioned in the first chapter of this essay, scientific theories are always open to be challenged, both in part and in whole, when new evidence presents itself. The evidence in both cases supports evolution; the difference is that different models of evolution are better supported by one kind of evidence than another.

The Cambrian Explosion in the second part of the argument (http://en.wikipedia.org/wiki/Cambrian_explosion) is a challenge, and much more worthy of discussion. The particular quote much-bandied by creationist websites that comes from Dawkins’ The Blind Watchmaker is:

“…the Cambrian strata of rocks, vintage about 600 million years, are the oldest ones in which we find most of the major invertebrate groups. And we find many of them already in an advanced state of evolution, the very first time they appear. It is as thought they were just planted there, without any evolutionary history. Needless to say, this appearance of sudden planting has delighted creationists.”

Note that the actual full quote is:

“Before we come to the sort of sudden bursts that they had in mind, there are some conceivable meanings of ‘sudden bursts’ that they most definitely did not have in.mind. These must be cleared out of the way because they have been the subject of serious misunderstandings. Eldredge and Gould certainly would agree that some very important gaps really are due to imperfections in the fossil record. Very big gaps, too. For example the Cambrian strata of rocks, vintage about 600 million years, are the oldest ones in which we find most of the major invertebrate groups. And we find many of them already in an advanced state of evolution, the very first time they appear. It is as though they were just planted there, without any evolutionary history. Needless to say, this appearance of sudden planting has delighted creationists. Evolutionists of all stripes believe, however, that this really does represent a very large gap in the fossil record, a gap that is simply due to the fact that, for some reason, very few fossils have lasted from periods before about 600 million years ago. One good reason might be that many of these animals had only soft parts to their bodies: no shells or bones to fossilize. If you are a creationist you may think that this is special pleading. My point here is that, when we are talking about gaps of this magnitude, there is no difference whatever in the interpretations of ‘punctuationists’ and ‘gradualists’. Both schools of thought despise so-called scientific creationists equally, and both agree that the major gaps are real, that they are true imperfections in the fossil record. Both schools of thought agree that the only alternative explanation of the sudden appearance of so many complex animal types in the Cambrian era is divine creation, and both would reject this alternative.”

Again, the tone is a bit more shrill than constructive, but its point is clear. The problem is one of a fossil gap, not one of an unexplainable feature of the fossil record. As we see with human fossil lineage, once attention has been drawn to a subject, studies and funding follow – now pre-Cambrian multi-cellular creature fossils have begun to accumulate. See the latter sections in the wikipedia link: http://en.wikipedia.org/wiki/Cambrian_explosion#How_real_was_the_explosion.3F. Still, the Cambrian Explosion was a particularly aggressive adaptive radiation, which leads to the question of what caused or allowed for it – continue on through the Wikipedia link for possible explanations of the new “niche” the radiation exploited.

Now that we’ve stated what evolution is and is not, we need to establish the evidence for evolution. I’ll present three different types of evidence: circumstantial evidence (evidence which fits well with the theory of evolution but does not directly prove it; i.e. evidence for which another plausible explanation may be available), direct evidence (evidence which lends directly to supporting evolution and not another theory), and experimental evidence (evidence from the lab which reproduces evolution or evolutionary adaptation). As with the previous chapter, please feel free to chime in, whether it’s to add more evidence, to provide an alternate explanation for evidence I’ve given, to refute the evidence, or to suggest reclassification. Additionally, if you have evidence to the contrary, let me know so I can address it in future chapters!

Please note that this evidence is not meant to be exhaustive – it’s a quick list of some of the most compelling evidence that is easily available. If more is needed, let me know!

Circumstantial Evidence

Phylogenetics is the area of study reconstructing the evolutionary “family tree” – that is, grouping species who are most related and determining common ancestors, then finding common ancestors for those, etc., to proceed up the tree. In the past, this was done mostly by comparing the way species looked and behaved, which could cause a lot of false starts. For example, ants and termites appear to be very similar in behavior and appearance, but ants are actually more closely related to wasps (order Hymenoptera), while termites are related closely to cockroaches (order Blattaria). More recently, however, philogeneticists have been able to provide more accurate and detailed reconstructions by sequencing mitochondrial genomes and ribosomal RNA sequences (the same DNA sequencing techniques used by courts to see if two people arerelated). In essence, this is like comparing millions of slightly different copies of the same book. The differences between copies of the books are not completely random – they follow a hierarchical structure (all copies with change A also have change B, and all copies with change C also have change B; thus we suspect change B came before either changes A or C). These are much more useful for building the family tree. The fact that we -can- build this family tree at all indicates that it is likely to have exist, which would imply that the species evolved through a “common descent”. However, DNA sequencing can only be performed on extant soft tissue (DNA isn’t preserved in fossils), so we can’t conclusively fit extinct species into a family tree this way, only note where we would expect them to fit.

The universal coding of DNA – i.e. DNA across all species is written in a single “coding language” – is evident in the fact that the same strings of DNA will produce the same proteins regardless of what species it’s in: bacterium or human, snail or whale. Completely foreign genomes can be ported into a new species (like the lab mice who glow like jellyfish). ATP is used as the “energy currency” by all species we know about; despite the complexity of the creatures or their place on the evolutionary family tree – that aspect of metabolism seems to have evolved very early in single-cell history. Opsins (light-sensing proteins) appear to have evolved independently on separate occasions but still perform the same function. A common source code, like common descent, is consistent with the evolutionary model, but admittedly it could also fit into some forms of a creationist model.

Atavisms are the reappearance of features lost in previous evolutionary steps (the coding gene exists but was flipped off in the species, then flipped back on by mutation in the individual). Examples we’ve observed (courtesy of wikipedia) include hind legs on snakes and whales, hind flippers on dolphins, extra toes on horses (modern horses have one, but horse fossils going back into archaic periods have more, up to the familiar total of five), and teeth in chickens. Examples of these are easily googleable, but let me know if you have any trouble finding them. In humans, long canine teeth, vestigial tails, and extra nipples that follow the milk line are the most common examples. One could conceivably dismiss these as random mutations rather than returns to a previous form, but this raises the question: why would a creator litter a species with latent genes? At the least, it seems unlikely.

Similarly, the shapes of developing vertebrate embryos seem to be atavistic. Though there is some initial difference in the shape of embryos, the shapes converge at a certain point, before diverging again as the species the embryos represent become more dissimilar. This image http://home.honolulu.hawaii.edu/~pine/book1qts/embryo-compare.jpg from Mayr is a frequently-used illustration of the similarity of the shapes, but comparisons were made as long ago as the middle of the 19th century. The similarity has led some to remark (more poetically than scientifically) that embryos seem to pass through the stages of their vertebrate family tree – fish, amphibian, reptile, then mammal. This shared morphology indicates the likelihood of a significant shared genetic heritage.

Reuse of features is one of the stronger circumstantial evidences for evolution. Among tetrapods (four legged creatures, including mammals, reptiles, amphibians, and even some fish), the pentadactyl (five-fingered) limb construction is a common trait – even those that don’t have five fingers (like the horse and dolphins) appear to have it in their genetic and fossil background. The common features are: a single bone in the proximal segment (upper arm), two bones in the distal segment (lower arm), followed by five series of palm bones and digits; but the features have been adapted to different uses in different creatures depending on the niche of the creature. This is especially evident among mammals (again, examples courtesy of wikipedia – http://en.wikipedia.org/wiki/Evidence_of_common_descent#Pentadactyl_limb):

In the monkey, the forelimbs are much elongated to form a grasping hand for climbing and swinging among trees.

In the pig, the first digit is lost, and the second and fifth digits are reduced. The remaining two digits are longer and stouter than the rest and bear a hoof for supporting the body.

In the horse, the forelimbs are adapted for support and running by great elongation of the third digit bearing a hoof.

The mole has a pair of short, spade-like forelimbs for burrowing.

The anteater uses its enlarged third digit for tearing down ant hills and termite nests.

In the whale, the forelimbs become flippers for steering and maintaining equilibrium during swimming.

In the bat, the forelimbs have turned into wings for flying by great elongation of four digits, while the hook-like first digit remains free for hanging from trees.

While this is consistent with a pentadactyl-limbed ancestor evolving into the creatures we know today, in a creationist model it leaves one to question why a creator would adapt structures from one creature to another, rather than building each as was best suited for their needs?

The human Chromosome 2 is a remarkable piece of evidence. Humans have 23 chromosomes; oddly enough all other hominidae (the great apes – our local branch of the family tree) have 24 chromosomes. On the face of it, this seems to undermine the idea that humans share a common ancestor with the other hominidae. Chromosome 2 in humans is fairly long – the second longest of all 23, and there is no chromosome of corresponding length in the other hominidae. On further examination, we see that chimpanzees have two chromosomes that we don’t (now called Chromosomes 2a and 2b), which add up to a length similar to our Chromosome 2, and the genes on their chromosomes 2a and 2b correspond to the same locations on our Chromosome 2. Even more tellingly, though, human Chromosome 2 has some very unusual distinctions: where chromosomes typically have a single centromere near the middle and telomeres on either end, Chromosome 2 has two centromeres, and a vestigial pair of telomeres in the middle, at the fusion point! These kind of mutation-induced oddities are to be expected in an evolutionary model, but seem an unlikely event in a creationist model. You can read more about Chromosome 2 here: http://en.wikipedia.org/wiki/Chromosome_2_(human) or http://en.wikipedia.org/wiki/Chimpanzee_genome_project

An endogenous retrovirus is a viral fossil within our DNA – a section of our genetic code that seems have been inserted by a virus in the distant past. Collectively, endogenous retroviri account for as much as 8% of the human genome. Most of this DNA is mutated junk data that cannot produce a protein, but there does seem to be involvement between some ERVs and autoimmune syndromes like multiple sclerosis. Some ERVs also seem to be useful during pregnancy, where they appear to suppress the mother’s immune system, thereby protecting the baby from being attacked by the mother. Some ERVs have successfully been “freed” from the human genome and reverted to retroviruses to prove that they were in fact RVs. Again, ERVs fit perfectly into an evolutionary model, but don’t seem to make sense in a creationist model – while some have use, why litter the genome with the rest, especially when they can have such negative effects? You can read more here: http://en.wikipedia.org/wiki/Endogenous_retrovirus

Non-coding DNA, (originally called “junk” DNA) is made up of much more than just ERVs; it’s estimated to compose 98% of the human genome. In some cases, the DNA has use beside coding (telomeres and centromeres are non-coding, as are master control genes), but much of it seems to be useless – studies have shown that portions of this non-coding DNA can be removed from lab mice with no discernible affect to the creatures. Like the ERVs (and the ERVs are a prime example of non-coding DNA), much of this code seems to be vestigial remainders of our ancestor species that produces no overwhelmingly negative effect that would cause it to be selected for editing out in mutation. Why would a creator litter our DNA with useless strands?

Direct Evidence

One of the most obvious sources of direct evidence is the fossil record, and in particular the so-called intermediate fossils (“so-called” because all fossils are intermediate to earlier and later species). Because these deserve so much attention, I’ll save them for their own chapter. Expect to see the fossil record for the horse, the whale, camelids, and the transition from dinosaur to bird. The key concept here is that the fossil record clearly shows the appearance and disappearance of different species, and the divergence of parent species into the modern species we see today. There is no reasonable explanation for the fossil record in a creation theory that does not include either evolution or a deceptive creator.

Another telling source of direct evidence is the abundance of vestigial organs and vestigial features common to all complex species, but which we see most frequently in humans (because we study ourselves in greater detail than other species). Again, these deserve special attention and will be treated in depth in the chapter dealing with Intelligent Design, but expect to see goosebumps, Jacobsen’s Organ, Darwin’s tubercle, our extra ear muscles, the plantaris muscle, our wisdom teeth, our third eyelid, the coccyx, our little toe, and our appendix show up as examples. Vestigial organs are markers of past evolution (just as mason’s marks help us to understand how castles and cathedrals were constructed), but they also argue against an all-powerful, intelligent creator. In some cases they would just seem to be sloppy handiwork, but in other cases (like our wisdom teeth and appendix) the vestigial organs not only have no useful modern purpose, but can cause us serious harm.

The Galapagos Finches (from which I derived my example in the first chapter), Silverswords (a Hawaiian cactus-like plant), and Drosophila (a genus of fruit fly) are all examples of adapative radiations. Adaptive radiation is a phenomenon that occurs most frequently in the aftermath of a mass extinction or when a creature is introduced to a new environment – essentially when a species encounters unexploited ecological niches. This is especially common in island chains (like the Galapagos and Hawaiian islands), where there are a variety of environments in close proximity; the first bird and plant species that are able to cross the ocean from their native environment adapt rapidly to fill all of the available niches. In many cases, these adaptations lead to speciation. See Darwin’s 14 finch species (http://en.wikipedia.org/wiki/Darwin’s_finches) which are sufficiently divergent to occupy four different genera, the Hawaiian Drosphila (http://www.nap.edu/openbook.php?record_id=10865&page=14) at 800 species in 2 genera, and the silversword alliance (http://waynesword.palomar.edu/ww0903b.htm) at 50 species in 3 genera for further details of their specific details. We can usually identify the parent species (which frequently still exists in its native location), making adaptive radiations neatly packaged synecdoches for evolution; i.e. they make good study subjects.

The Cichlid fish of Lake Victoria are a recently studied example of adaptive radiation. The Cichlids are a family of fish that include as wide a range as tilapia, oscar, angelfish, and peacock bass across the world; iIn Lake Victoria there are at least 500 species of cichlids which, while sharing the several features common to all cichlids, span a wide variety of colors and shapes. As in the other cases mentioned above, we’ve been able to identify the reason for the changes leading to speciation: Even though Lake Victoria is a single large lake (a -very- large lake), the different levels of clarity and light penetration in different parts of the lake favor different colors and sizes of fish. (http://www.arn.org/blogs/index.php/literature/2008/10/09/cichlid_fish_another_textbook_example_of). A separate phylogenetic study that sampled the DNA of 14 representative species identified the ancestor species as one that swam in the East African streams when Lake Victoria was dry 12,000 years ago.

Observed adaptation and observed evolution can be as powerful a source of evidence as the fossil record. Examples include:

The Atlantic Tomcod (http://en.wikipedia.org/wiki/Atlantic_tomcod) of the Hudson River has adapted a genetic tolerance for PCB, a toxin dumped in the river from 1947 through 1976 (when it was banned) which does not degrade quickly. A minor mutation in the tomcod (a deletion of 6 pairs) that allows the fish to survive a level of the toxin that is lethal to other species already occurs in a small fraction of tomcod who swim in other waters (indicating it’s a frequent mutation), but now appears in 99% of Hudson River tomcod. The Hudson River tomcod handle the toxin so well that there is concern over their ability to survive if the toxin is removed from the river.

Nylon-eating bacteria (http://en.wikipedia.org/wiki/Nylon-eating_bacteria) are a strain of bacteria capable of digesting byproducts of nylon production, though these chemicals are not known to have existed prior to the invention of nylon in 1935. To quote wikipedia directly:

“In 1975 a team of Japanese scientists discovered a strain of Flavobacterium, living in ponds containing waste water from a nylon factory, that was capable of digesting certain byproducts of nylon 6 manufacture, such as the linear dimer of 6-aminohexanoate, even though those substances are not known to have existed before the invention of nylon in 1935. Further study revealed that the three enzymes the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by other Flavobacterium strains (or any other bacteria for that matter), and not effective on any material other than the manmade nylon byproducts.”

This ability has been recreated in lab by exposing similar strains to the same environment; interestingly the mutations that eventually allowed the strains to adapt produced the same results, but were different than those in the original strain.

Radiotrophic fungi (http://en.wikipedia.org/wiki/Radiotrophic_fungus) are a species of black slime mold found in the destroyed Chernobyl reactor that have adapted a method of producing chemical energy from gamma radiation. These species do poorly in the absence of extreme radiation and this level of radiation is not found naturally, so this is suspected to be an entirely unprecedented adaptation.

The Blackcap – a European variety of warbler – appears to be on the verge of speciation. Recently a fraction of the migratory flock (which is native to northern continental Europe) split off from the rest and developed a new habit of wintering in southern England instead of across the Alps along the Mediterranean. These two new flocks tend not to interbreed any longer, and it is expected they’ll begin to diverge genetically in a few dozen generations.

The Hawthorn Fly seems to have recently finished speciating. Apples are a non-native species to North America, and after their introduction in the 18th century some hawthorn flies preferred the fruit of the apple tree, while some retained a preference for hawthorn fruit. As of now there is very little interbreeding between apple flies and hawthorn flies (4-6% incidence of hybridization), and there is significant difference in their DNA.

It’s fair wonder how to draw the line between adaptation and speciation, especially since viable hybrids are possible between recently diverged sexually-reproducing species (like the lion and tiger, or like dingos, coyotes, and wolves). Among asexually-reproducing creatures we don’t even have the metric of hybridization and have to judge purely by genetic drift. What’s important to understand is that there -is- no hard line between adaptation and speciation. The theory of evolution doesn’t suggest that rapid and dramatic speciation is typical, but rather that creatures who adapt to different niches will, for one of a variety of reasons, lose the ability or desire to interbreed with each other. As breeding groups diverge, mutations that make the reproductive rounds in one group and not the other will cause genetic drift between them, and eventually hybrids will be genetically non-viable. The species listed above are evidences at different points along that process.

Experimental Evidence

The Silver Fox experiment is a breeding program started in Russia in the 50’s, in which the fox was intentionally domesticated (bred for docility and a good temperament around humans, since this is a feature with a genetic foundation) to replicate the unintentional long-term domestication of wolves into the modern family dog. An unexpected result of the experiment was that the domesticated foxes took on other, un-selected-for features common to dogs, like floppy ears, a curly tail, spotted markings, a reduced musk, and biannual estrus. These traits do not normally appear appear among silver foxes. This is evidence that even when a niche selects for only a single feature, multiple distinctive features may diverge.

Sticklebacks are a popular fish among experimental biologists. There are over forty different morphologies (shapes/colors) living in both saltwater and freshwater environments that appear to be radically different species. They typically will not interbreed, or cannot interbreed for reasons of physical incompatibility. However, like modern dogs with size differences, the species can be artificially hybridized and appear to be what is called a “ring species”, which (like the hawthorn fly and blackcap) is a creature on the verge – sometimes for a very long time – of speciation. It is possible to trace the sticklebacks’ adaptive histories to a single morphology during the glacial retreat at the end of the last ice age, when they found new niches in the uncovered freshwater lakes. One of the features of the freshwater subspecies is an increased tolerance to cold water that would kill the marine species. By keeping samples of the marine species in successively colder freshwater, biologists were able to reproduce the tolerance of the freshwater subspecies in a marine subspecies within three generations.

Theodore Garland continues to run a long-term experiment with laboratory house mice. To quote wikipedia directly:

“In 1993, Theodore Garland, Jr. and colleagues started a long-term experiment that involves selective breeding for high voluntary activity levels on running wheels. This experiment also continues to this day (> 50 generations). Mice from the four replicate “High Runner” lines evolved to run 3 times as many running-wheel revolutions per day as compared with the four unselected control mice groups, mainly by running faster than the control mice rather than running for more minutes/day.

The HR mice exhibit an elevated maximal aerobic capacity when tested on a motorized treadmill and a variety of other traits that appear to be adaptations that facilitate high levels of sustained endurance running (e.g., larger hearts, more symmetrical hindlimb bones). They also exhibit alterations in motivation and the reward system of the brain.”

An even more convincing experiment is Richard Lenski’s e. coli experiment, which has run past 50,000 generations (http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment). To understand the significance, you really have to read through the link, but the gist of it is as follows: Because E. coli reproduces asexually, the only genetic changes introduced to their successive generations are through mutation. Because E. coli can be frozen indefinitely, generations at any point during the experiment can be archived to maintain a “fossil” history, which can be revived and rerun in the future. In Lenski’s experiment there were a number of significant mutations, but the most surprising came after about 32,000 generations, when one of his colonies developed the entirely new ability to metabolize citrate in oxygen – essentially the ability to live on a new food source. To quote wikipedia (again):

“Examination of samples of the population frozen at earlier time points led to the discovery that a citrate-using variant had evolved in the population at some point between generations 31,000 and 31,500. They used a number of genetic markers unique to this population to exclude the possibility that the citrate-using E. coli were contaminants. They also found that the ability to use citrate could spontaneously re-evolve in populations of genetically pure clones isolated from earlier time points in the population’s history. Such re-evolution of citrate utilization was never observed in clones isolated from before generation 20,000. Even in those clones that were able to re-evolve citrate utilization, the function showed a rate of occurrence on the order of once per trillion cells. The authors interpret these results as indicating that the evolution of citrate utilization in this one population depended on an earlier, perhaps non-adaptive “potentiating” mutation that had the effect of increasing the rate of mutation to citrate utilization to an accessible level (with the data they present further suggesting that citrate utilization required at least two mutations subsequent to this “potentiating” mutation).”

Unfortunately, it’s difficult to imagine a controlled experiment that would reproduce major evolutionary change in a vertebrate, like inducing a colony of reptiles to sprout feathers and become birds. Those kinds of changes require thousands, even millions of generations, which in complex creatures means thousands or millions of years (not to mention the number of creatures you’d have to maintain to provide a sample big enough for that series of mutations to have a chance of occurring and taking hold. Fruitflies, fish, and bacteria are the evolutionary scientist’s friend, and even then the changes are subtle, like the differences between two kinds of ant, rather an ant and a wasp. In a later chapter I’ll address this problem of experimental evidence more closely. For now, it should suffice to say that evolution has been experimentally demonstrated in simple organisms, and it’s been observed in more complex organisms. Most of the evidence that exists, both from contemporary and historical sources, supports the evolutionary model wherever we look for it. What does not directly support the theory of evolution does not refute it. The same cannot be said in any meaningful way for creationism.

There’s a very accurate, but also somewhat snarky definition of evolution floating around the internet – here, for example: http://i.imgur.com/2byyo.jpg. The problem is that as accurate as it is, it isn’t particularly useful or engaging. It’s liable to make a small group of people chortle smugly and most everyone else click away. We’ll have to run on a bit longer than the 12 points in the image, but let’s try to talk about this a little more personally and answer the question “What is Evolution?”

Evolution is an idea that says creatures change. From generation to generation the change may be small, but over tens or hundreds of generations the changes can be as significant as branching into a new species.

(It’s important to note here that the concept of a “species” is a difficult one, because it’s attempting to apply our concepts of categorization on a reality that can be fuzzy around the edges. Within species that reproduce sexually (like us!), a handy rule of thumb is that if the creatures can interbreed successfully and regularly produce fertile offspring of both sexes, then they are members of the same species. In creatures that don’t reproduce sexually – especially micro-oganisms – the defining lines between species becomes much more difficult to draw. More here, if you’re interested: http://en.wikipedia.org/wiki/Species#Definitions_of_species )

The idea of evolution says that over generations, creatures adapt to fill roles or niches in the environment, or are weeded out as those niches are eliminated. Let’s consider as an example a flock of birds that crosses a mountain range one particularly good summer, migrating to a new environment mostly similar to their old. However, in addition to their regular food supply of berries and grubs, in this environment the birds encounter a seed that is very nutritious, but also comes in a thick shell. Within this flock of birds there is some variety – among other differences, some of those birds have stronger beaks and some have weaker beaks. The birds with the weaker beaks aren’t able to crack the shells of these new seeds, so they rely on their berries and grubs, while the birds are able to enjoy all three – seeds, grubs, and berries. The birds with the stronger beaks have a better, more stable, more nutritious food supply, so in general they will be healthier, and in general they will have more eggs which hatch with a better chance of survival. Because a strong beak is a genetic factor, their hatchlings are more likely to also have strong beaks. Eventually over a number of generations, the birds with the stronger beaks are likely to outnumber (and potentially completely replace) the birds with the weaker beaks.

Let’s say, too, that this same flock of birds has some rather bright-colored feathers. In their previous environment they had few predators, and brighter feathers were a sign of health, so the she-birds were most interested in the he-birds with the bright feathers. But on this side of the mountains there are hawks with excellent color vision, and the birds with the brightest feathers are the most likely to be eaten (and thus the least likely to have a large, healthy brood of chicks). Even if the she-birds still prefer the brighter birds, the predation of the hawks will drive down the population of the brightest birds while the birds with duller feathers will thrive. (Eventually it’s likely that the she-birds who are interested in duller birds will be more common, since those who prefer bright he-birds are more likely to have their children eaten by hawks, so they won’t successfully pass on their genes.)

It can be said that the environment has “selected” for birds with stronger beaks and duller feathers, in the similar way that a dog breeder might select for longer coats or shorter legs over several generations. There is no intent in natural selection of course, only the statistical likelihood that the creatures most suited for an environment are the ones who will have the best chance for survival.

Where do these changes come from? Why might one bird from the same brood have a stronger beak, and another have duller feathers? The answer is DNA. In sexually reproducing creatures, each conception is a toss of the dice: 50% of the mother’s DNA selected at “random”, and 50% of the father’s, are combined together. Most of us studied meiosis in school, so it’s enough to link to refresher here: http://en.wikipedia.org/wiki/Meiosis . In general, two unrelated humans share about 99.9% of their 3 billion base pairs, and the remaining 3 million base pairs are organized into about 10,000 or so genes. If those two unrelated people have completely different genes (this is unlikely), there are about 10 thousand squared, or 100 million possible combinations of genes their offspring can have. If there are an average of 4 different types for each gene (there are more), one could say that there are 10 thousand to the fourth, or 10 quadrillion different possible combinations of human DNA. This doesn’t account for point mutation, which is as common as cancer. Minor disruptions to our DNA – errors in copying, extra copy and pasting, damage caused by free radicals and radiation or foreign substances (e.g. Thalidomide babies) can alter the gametes (sperm and eggs) which will join to become the next generation. In most cases, genetic damage is either too minor to have any advantage or disadvantage, or the damage is severe enough to render the creature infertile or unlikely to reproduce. Occasionally, the result is more striking, but nominal (see, for example, the introduction of blue eyes to humanity: http://en.wikipedia.org/wiki/Eye_color#Blue), and even more rarely it is helpful (like the ability to digest lactose as adults: http://en.wikipedia.org/wiki/Lactose_intolerance#History_of_genetic_prevalence).

You may say at this point that you accept that these differences are enough to form new races (among people) or breeds (among dogs), but not enough to form new species. You’ll require more evidence, and that’s understandable – it’s coming in future installments. For now, just understand two things: 1) If two groups of the same species are continuously able to interbreed, they are unlikely to speciate. If our birds described above were able to fly back and forth across the mountains to mingle with the other flocks, they would not be likely to form a new species. Humans have been a relatively mobile creature for quite a long time, but before that was the case there is evidence that they did speciate, and there were multiple groups of different species of humans existing simultaneously in different environments (http://en.wikipedia.org/wiki/File:Humanevolutionchart.jpg).

What’s important to understand, though, is that the idea of evolution does not suggest you are likely to see a new species form inside of a stable population. If our birds speciated as they grew stronger beaks and duller feathers, it would not be because of an “Adam and Eve” bird couple that appeared by happenstance among the flock and their children’s incestuous relationships. The environment would drive the entire flock to the new species over many generations as the weaker-beaked birds died faster in harsh winters and the hawks ate the brightly-colored hatchlings. It would only be by comparison to the flocks across the mountains that you would see a substantial difference.

Evolution is a theory, just as gravity is a theory, as elementary chemistry and electromagnetism are theories, and as string theory is a theory. A “theory” in scientific parlance may be a fact in regular conversation, or it may be a wild speculation. A “theory” is only a model for explaining things, and it can be backed by centuries of data and research, or it can be wholly unsubstantiated. Science refers to even “proven” models as theories instead of facts, though, because the models are in a constant state of revision as new data is received. In many theories, this revision is minor and around the edges – we understand the core of elementary chemistry and electromagnetism very well, and rely upon that understanding in our day to day life. Research there generally expands the periphery of our understanding; we don’t expect to see those theories completely overturned soon, or really ever. Our understanding of gravity is much more uneven – we know pretty well how it works, but understand very little of why it works, and the theory of gravity in that regard seems to change dramatically every few decades. The theory of evolution, as scientific models go, is considered to be extremely robust and well-supported. At this point, less work is being done to substantiate evolution because the “how” and “why” of it are so well understood. Much more work is being done to fill in the gaps of history – to join the fossil record between the branches and the twigs on the tree of life – and to find new ways to apply evolutionary theory in a useful way, like producing a species of micro-organisms that eats garbage and excretes fuel.

Evolution is NOT an explanation for the origin of the universe or even life. Evolution has nothing to say about the Big Bang – that is another field of science entirely: cosmology. Whether or not the Big Bang Theory is the best model for the beginning of the universe does not affect the theory of evolution. Similarly, whether life originated in a lightning-struck pool of murky water on primordial earth, or was carried in by comets from other worlds, or was deliberately placed on earth by ancient astronauts or God or gods does not affect the theory of evolution. Evolution only says that life will adapt to its environment because of natural selection; it does not include a model for genesis. Many people with a particular view on evolution also have particular view on how life began, but it is also true that they tend to have a particular view on the ultimate future of life (and especially human life) on earth – another topic on which the theory of evolution has nothing to say.

Evolution is NOT a philosophy. The Catholic Church officially espouses evolution. There is no official overarching Buddhist stance on evolution, but generally Buddhist thought considers it compatible, or irrelevant. There is a trend to speak of Darwinism as a school of philosophy rather than a collection of scientific theories (its original, and useful meaning), conflating it with elements of philosophical naturalism, utilitarianism, and Spencerism, and thereby to tie it into Nazi ideology and breeding programs (which are in fact the opposite of natural selection and more akin to husbandry). One can be a theist or an atheist and subscribe to the theory of evolution. One can accept evolution and be a communist (though communism, like the nazi breeding program, is actually an example of unnatural selection) or a staunch capitalist (it is easy to argue that the “market” practices a model of natural selection). One can be selfish or altruistic and find evolutionary support for their stance. Evolution has nothing to to say, either positively or negatively, about morals or any particular morality beside offering a model that might explain the origin of those morals.

So, now that we understand what evolution is, we can move on to looking at the evidence for and against it to see if it’s an accurate model.

I hope to continue to post at least once a week. Future topics are likely to be

2. What Proof Exists?3. Intermediate Fossils4. Why Are There Still Monkeys?5. Can We Prove Evolution If We Can’t Observe It?6. Why Not Intelligent Design?

But if you have questions you think need to be answered, let me know! I’ll be happy to change those plans if there’s some aspect of evolutionary theory you think is particularly weak that I don’t plan to cover.

Please comment! Let me know if I’ve made any mistakes or overlooked important points. I invite both conversation and debate, and understand the difference between the two.